Proteomic characterization of the liver of Nellore cattle divergent for feed efficiency

Author(s)

Leydiana Duarte Fonseca

• Document type: Doctoral Thesis
• Press: Pirassununga.
• Institution: Universidade de São Paulo (USP). Faculdade de Zootecnica e Engenharia de Alimentos (FZE/BT)
• Defense date: 2018-10-16

Examining board members

Joanir Pereira Eler; Luiz Lehmann Coutinho; José Bento Sterman Ferraz; Luciana Correia de Almeida Regitano; Saulo da Luz e Silva

• Advisor: Joanir Pereira Eler; Heidge Fukumasu

Abstract

Feeding is one of the most relevant cost of beef cattle production and improving nutrient utilization efficiency is essential for the viability of production, given the current scenario of increasing demand for animal protein and highly competitive market. In this context, proteomics appears as an important tool in the search for alternatives that increase the feed efficiency (FE) of beef cattle. Thus, the aim of this work is to characterize the hepatic proteome of beef cattle selected for divergent FE. Ninety-eight animals were evaluated in a previous project, and six individuals with low feed efficiency (LFE) and six with high feed efficiency (HFE) had liver samples collected at slaughter, frozen in liquid Nitrogen and stored in a freezer at -80 °C. After protein extraction and precipitation, the samples were processed by two different approaches: digested with trypsin in solution and analyzed in a high efficiency liquid chromatograph coupled to the mass spectrometer (LC-MS/MS); and previously separated in gel for further digestion and analysis (GeLC-MS/MS). Data acquired by LC-MS/MS were analyzed with MaxQuant software against the Bos taurus and Bos indicus Uniprot databases for proteins identification and the results analyzed with Perseus software. The data obtained by GeLC-MS/MS were analyzed with the softwares Mascot Distiller and X! Tandem and validated in the Scaffold Q+, against Bos taurus Uniprot database and results analyzed with the softwares Scaffold Q+ and Perseus. For the LC-MS/MS approach, 376 proteins were quantified and submitted to differential abundance analysis and co-expression networks by WGCNA, identifying 42 differentially abundant proteins (DAPs, p < 0.05) and three modules significantly associated with FE. For the GeLC-MS/MS approach, 102 proteins were quantified, of which five were DAPs (p-value < 0.05). Three DAPs were common to both proteomics approaches. Proteins negatively associated with FE were mainly related to lipid synthesis, degradation of fatty acids, cytochrome P450 system enzymes and oxidative processes. On the other hand, proteins positively related to FE were mainly involved in protein processing and folding, maintenance of the integrity and restoration of the cellular cytoskeleton. In both groups were also identified proteins that play a role on the immune system and inflammatory response. These results prove previous experiments of the group and demonstrate the existence of difference between liver proteomes of efficient and inefficient animals. (AU)

• FAPESP's process: 14/04937-0 - Comparative proteomic analysis of liver Nelore cattle males of high and low feed efficiency
• Grantee: Leydiana Duarte Fonseca
• Support Opportunities: Scholarships in Brazil - Doctorate